DSSR-enabled G4 identification/annotation: PDB entry 2lk7
Summary information and primary citation
- PDB-id
- 2lk7
- Class
- DNA
- Method
- NMR
- Summary
- Monomer-dimer equilibrium for 5'-5' stacking of propeller-type parallel-stranded g-quadruplexes: NMR structural study
- Reference
- Do NQ, Phan AT (2012): "Monomer-Dimer Equilibrium for the 5'-5' Stacking of Propeller-Type Parallel-Stranded G-Quadruplexes: NMR Structural Study." Chemistry. doi: 10.1002/chem.201103295.
- Abstract
- Guanine-rich sequence motifs, which contain tracts of three consecutive guanines connected by single non-guanine nucleotides, are abundant in the human genome and can form a robust G-quadruplex structure with high stability. Herein, by using NMR spectroscopy, we investigate the equilibrium between monomeric and 5'-5' stacked dimeric propeller-type G-quadruplexes that are formed by DNA sequences containing GGGT motifs. We show that the monomer-dimer equilibrium depends on a number of parameters, including the DNA concentration, DNA flanking sequences, the concentration and type of cations, and the temperature. We report on the high-definition structure of a simple monomeric G-quadruplex containing three single-residue loops, which could serve as a reference for propeller-type G-quadruplex structures in solution.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 3(-P-P-P)
Cartoon-block schematics in six views (download the tarball)
List of 3 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.086 type=planar O+ nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15 2 glyco-bond=---- sugar=---- groove=---- planarity=0.096 type=planar O+ nts=4 GGGG A.DG4,A.DG8,A.DG12,A.DG16 3 glyco-bond=---- sugar=---- groove=---- planarity=0.117 type=planar O+ nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG17
List of 1 G4-helix
In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.
Helix#1, 3 G-tetrads, INTRA-molecular, with 1 stem
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG8,A.DG12,A.DG16 3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG17 step#1 pm(>>,forward) area=12.32 rise=3.30 twist=29.7 step#2 pm(>>,forward) area=13.60 rise=3.49 twist=28.9 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG7,A.DG8,A.DG9 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG11,A.DG12,A.DG13 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG15,A.DG16,A.DG17 |
| 2 stacking diagrams | |
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15 |
|
2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG8,A.DG12,A.DG16 |
List of 1 G4-stem
In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.
Stem#1, 3 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 3(-P-P-P)
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG7,A.DG11,A.DG15 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG8,A.DG12,A.DG16 3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG9,A.DG13,A.DG17 step#1 pm(>>,forward) area=12.32 rise=3.30 twist=29.7 step#2 pm(>>,forward) area=13.60 rise=3.49 twist=28.9 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG7,A.DG8,A.DG9 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG11,A.DG12,A.DG13 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG15,A.DG16,A.DG17 loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT6 loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT10 loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT14 |